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29  structures 3324  species 4  interactions 6097  sequences 79  architectures

Family: SUI1 (PF01253)

Summary: Translation initiation factor SUI1

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SUI1 Edit Wikipedia article

SUI1
PDB 1d1r EBI.jpg
NMR solution structure of E. coli yciH gene.
Identifiers
SymbolSUI1
PfamPF01253
InterProIPR001950
PROSITEPDOC00862
SCOPe2if1 / SUPFAM

In molecular biology, the single-domain protein SUI1 is a translation initiation factor often found in the fungus, Saccharomyces cerevisiae (Baker's yeast) but it is also found in other eukaryotes and prokaryotes as well as archaea. It is otherwise known as Eukaryotic translation initiation factor 1 (Eukaryotic translation initiation factor 1 eIF1) in eukaryotes or prokaryotic initiation factor-3 or YciH in bacteria.[1]

Function

SUI1 is a translation initiation factor that directs the ribosome to the translation start site, helped by eIF2 and the initiator Met-tRNAiMet.[2] SUI1 ensures that translation initiation commences from the correct start codon (usually AUG), by stabilizing the pre-initiation complex around the start codon. SUI1 promotes a high initiation fidelity for the AUG codon, discriminating against non-AUG codons.[3] .

pIF3 is not universally found in all bacterial species. However, in E. coli, it is required for the 30S subunit to bind to the initiation site in mRNA. In addition, it has several other jobs including the stabilization of free 30S subunits, enables 30S subunits to bind to mRNA and checks for accuracy against the first aminoacyl-tRNA. It also allows for rapid codon-anticodon pairing for the initiator tRNA to bind quickly. IF3 is required by the small subunit to form initiation complexes, but has to be released to allow the 50S subunit to bind.

Structure

The primary structure of the SUI1 protein is made up of 108 amino acids. The protein domain has a structure made of a seven-bladed beta-propeller and it also contains a C-terminal alpha helix.[4] Homologues of SUI1 have been found [5] in mammals, insects and plants. SUI1 is also evolutionary related to proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.[4]

References

  1. ^ Prokaryotic+Initiation+Factor-3 at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. ^ Yoon HJ, Donahue TF (January 1992). "The suil suppressor locus in Saccharomyces cerevisiae encodes a translation factor that functions during tRNA(iMet) recognition of the start codon". Molecular and Cellular Biology. 12 (1): 248–60. PMC 364089. PMID 1729602.
  3. ^ Martin-Marcos P, Cheung YN, Hinnebusch AG (December 2011). "Functional elements in initiation factors 1, 1A, and 2β discriminate against poor AUG context and non-AUG start codons". Molecular and Cellular Biology. 31 (23): 4814–31. doi:10.1128/MCB.05819-11. PMC 3232919. PMID 21930786.
  4. ^ a b Herrmannová A, Daujotyte D, Yang JC, Cuchalová L, Gorrec F, Wagner S, Dányi I, Lukavsky PJ, Valásek LS (March 2012). "Structural analysis of an eIF3 subcomplex reveals conserved interactions required for a stable and proper translation pre-initiation complex assembly". Nucleic Acids Research. 40 (5): 2294–311. doi:10.1093/nar/gkr765. PMC 3300007. PMID 22090426.
  5. ^ Fields C, Adams MD (January 1994). "Expressed sequence tags identify a human isolog of the suil translation initiation factor". Biochemical and Biophysical Research Communications. 198 (1): 288–91. doi:10.1006/bbrc.1994.1040. PMID 7904817.
This article incorporates text from the public domain Pfam and InterPro: IPR001950

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Translation initiation factor SUI1 Provide feedback

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001950

In budding yeast (Saccharomyces cerevisiae), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation [PUBMED:1729602]. SUI1 is a protein of 108 residues. Close homologues of SUI1 have been found [PUBMED:7904817] in mammals, insects and plants. SUI1 is also evolutionary related to:

  • Hypothetical proteins from bacteria such as Escherichia coli (yciH) or Haemophilus influenzae (HI1225).
  • Hypothetical proteins from archaea such as Methanococcus jannaschii (MJ0463).

Two eukaryotic proteins also seem to contain a C-terminal SUI1-like domain. These are:

  • Density-regulated protein (gene: DENR). This protein is found in mammals, insects, nematodes, plants and fungi.
  • Ligatin (gene: LGTN). This protein is found in mammals and insects.

Gene Ontology

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Domain organisation

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Alignments

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(380)
Full
(6097)
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(12638)
NCBI
(12600)
Meta
(472)
RP15
(1552)
RP35
(3575)
RP55
(5440)
RP75
(7267)
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  Seed
(380)
Full
(6097)
Representative proteomes UniProt
(12638)
NCBI
(12600)
Meta
(472)
RP15
(1552)
RP35
(3575)
RP55
(5440)
RP75
(7267)
Alignment:
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  Seed
(380)
Full
(6097)
Representative proteomes UniProt
(12638)
NCBI
(12600)
Meta
(472)
RP15
(1552)
RP35
(3575)
RP55
(5440)
RP75
(7267)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 380
Number in full: 6097
Average length of the domain: 75.60 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 35.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.5 25.5
Trusted cut-off 25.5 25.5
Noise cut-off 25.4 25.4
Model length: 77
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 4 interactions for this family. More...

Ribosomal_S17 Ribosom_S12_S23 Ribosomal_S8 KOW

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SUI1 domain has been found. There are 29 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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